Reprogrammed
by Queen of Fairyland
Summary: Sequel to The Program. Rodney & John escaped from the Ancient machine on Lorania but it's effects on their personality have remained. How will they cope with the change when there appears to be no way to fix it? And how serious is the damage?
1. Chapter 1

A/N: So it's been _forever_ since I posted 'The Program' and I've still yet to finish the sequel, and probably wont for a while, as I've made other commitments in terms of writing, and have work and uni as well. But I thought I would start posting it anyway.

* * *

It was only in the infirmary, the day after they had returned, that Elizabeth began to notice the changes.

It was in the way Rodney sat casually on one of the beds, showing no outward concern, when he should have been talking a mile a minute as he panicked about possible brain damage.

It was there in how John let a hint of his anxiety slip into his expression, and how he sat on the edge of the bed, body tense and nervous.

It was then that she wondered how on earth she'd missed it when they'd returned the day before.

Elizabeth took a steady step into the infirmary which was completely at odds with how she felt. "So what did you find?" she asked Beckett as she walked over to them, file folder in hand. He hesitated, glancing at Sheppard and then McKay. Beckett had obviously noticed the difference too.

"Nothing," he answered.

"Nothing?" Rodney asked with a raised eyebrow.

"Nothing at all," Beckett replied, letting his frustration creep into his tone.

"How can you not have found anything?" Sheppard asked in disbelief. "He rearranged our brains!" he exclaimed.

"John," Elizabeth said placatingly, disquieted by the fact she was having to use that tone with him.

"Sorry," he muttered. "It's just…it feels…"

"Wrong," Rodney finished for him. "Definitely wrong." Sheppard nodded in agreement.

"Well I'm sorry, but I can't find anything physically wrong with you," Beckett said apologetically.

"That isn't good enough," John said lowly.

"We've solved the nature versus nurture argument at least," Rodney shrugged. "If that's any consolation."

"What do you mean?" Elizabeth asked as Sheppard glared at him.

"Well it would seem personality has no root in biology if ours have been changed and there's no biological difference," he explained.

"That's fantastic Rodney, that'll help me sleep at night," Sheppard muttered.

"I'm sorry, I don't know what else I can do for you," Beckett said remorsefully.

"Don't worry Carson, you've done all you can," Rodney said to Beckett, with a reassuring pat to his shoulder. "Does this mean we're free to go?"

"I don't see why not," Beckett said with a sigh. "But I want you back every six hours," he added.

"O-kay then," he said with a smile. "I'll be in the labs if anyone needs me," he said before hopping off the bed and walking out of the infirmary. Sheppard watched him go with a frown.

"What?" Elizabeth asked.

"Nothing," Sheppard replied dismissively. "See you in six hours Carson," he said before leaving.

"What do we do now?" Elizabeth asked once he was out of earshot.

"I've no idea," Beckett answered.

* * *

Elizabeth looked up at the tentative knock on her office door.

"Doctor Zelenka," she smiled. "Something I can do for you?"

Radek bit his lip before nodding and taking a step inside. She looked at him expectantly but he glanced meaningfully at the open door.

"Something on your mind?" she asked, once she had closed the door.

"Yes," he took a breath. "Is concerning recent mission," he paused again. "Rodney is being quiet," he blurted.

Elizabeth smiled reassuringly, trying to assuage Radek's concerns, "I doubt-"

"And patient, and polite, and nice!" he exclaimed. "It is not right, is not natural. And is making science staff uncomfortable," he finished.

"We are doing everything we-"

"Sorry, but Rodney says the tests found nothing. He seemed unconcerned. It's not normal!" he protested. "What is it that is being done?" he questioned.

"We have people going through the archives. And as soon as we can be certain the Wraith have abandoned we will return to Lorania to investigate further," she explained.

"The device was destroyed, and it could take years to go through Atlantis' database, if there's anything there at all.!"

"What's your point Doctor?" she snapped. She waited before adding, "It's all we've got right now. If you come up with any better ideas, let me know."

* * *

"Christ Rodney, what's wrong with you?!"

Rodney looked up from his laptop and raised an eyebrow at Sheppard.

"Colonel," he greeted him.

"No, seriously, can you explain to me what the hell it is that you're doing?" he demanded.

"Well, at the moment," he span the laptop round, "I'm playing solitaire."

"Rodney," Sheppard growled.

"If I knew what was wrong with me Sheppard, I'd let you know, not to mention Beckett, so that we could get it fixed, but as it is-"

"You've given up caring," Sheppard accused.

"I'm just getting on with things Colonel!" he exclaimed. "What else is there to do?"

"I don't know Rodney," Sheppard said angrily, stalking towards the bench Rodney was seated at. "But you're the resident genius around here! You should be doing something!"

"And what exactly am I supposed to do Colonel?!" Rodney demanded.

"Freak out, at the very least!" Sheppard shouted.

"Oh so that's your problem, you don't like the fact that - God forbid - you're letting everyone see how you feel. Jesus Sheppard, welcome to the human fucking race!" he shouted. Sheppard spluttered for a minute before taking a step back. Rodney smirked at his retreat, and before he had a chance to blink Sheppard's fist collided with his face.

* * *

"I can't believe we're actually sneaking into the infirmary, this is ridiculous," Rodney muttered as he kept watch, as well as he could with his head tilted back.

"Shut up," Sheppard hissed from inside the supply cupboard.

"I don't know why I'm even helping you, you hit me!"

"Only because you made me touch that stupid machine on Lorania, which gave me a personality transplant," he muttered angrily as he shoved some cotton wool and pain killers into Rodney's free hand.

"What's this for?" he asked, holding up the cotton wool.

"You've got a split lip," he muttered, before heading towards another area of the infirmary.

"Where are you-?"

"Ice pack," he answered as he rooted around for one, eventually giving up and grabbing some cloth before rooting around the freezer to get some ice.

"That's gonna leave some bruise huh?" Rodney asked when he returned. Sheppard glared as he put the make shift ice pack over his eye.


	2. Chapter 2

A/N: So it's been _forever_ since I posted 'The Program' and I've still yet to finish the sequel, and probably wont for a while, as I've made other commitments in terms of writing, and have work and uni as well. But I thought I would start posting it anyway. So keep in mind, this story may abruptly stop at some point :(

Thanks to everyone who reviewed the last chapter and those of you who read it as well.

* * *

When the call from Elizabeth for them to go the briefing room came over the radio later, Sheppard groaned inwardly. When he spotted Rodney walking into the room just ahead of him with cotton wool still stuck up his nose he groaned out loud.

He heard Elizabeth's shocked "What happened?" just before he entered, and contemplated turning round again. Unfortunately Caldwell spotted him, his eyes darting to Sheppard's black eye and quickly put two and two together.

"I think the answer to that question has just arrived Doctor Weir," he said with a hint of a smirk as Sheppard entered the briefing room.

"I s'pose you walked into a door too?" Beckett asked with a glare.

"Funnily enough-" he began.

"Don't even try it John," Elizabeth said sternly. There was a pause where everyone in the room looked at John and Rodney expectantly.

"We may have had a slight disagreement," Sheppard said eventually. He winced as Teyla gave them a disapproving look, whilst Ronon just smirked.

"Way to keep it a secret there Colonel," Rodney muttered.

"Over what?" Caldwell asked, perhaps a little too eagerly. Elizabeth looked at him with a raised eyebrow. "Oh don't tell me you're not interested as to why the military leader and chief scientist of Atlantis resorted to fists."

"He has a point gentleman," Elizabeth turned to them expectantly.

"Well it's going to sound stupid now-"

"Colonel," Elizabeth said sternly.

"We were having an argument about the fact that I'm not hysterical and Sheppard is," Rodney explained quickly. "And then he hit me," he added. Sheppard kicked him.

"You're kidding," Caldwell said.

"Nope, hysterical like a little girl," Rodney said with a smirk, Sheppard hit him round the back of the head.

"Have I missed something?" Caldwell asked.

"Yes Colonel, which was exactly why I called this meeting," she said, and they began to explain the situation.

* * *

As they exited the debriefing room, John hung back for a moment until the room had cleared of all but Elizabeth and Caldwell.

"Sir," he said as Caldwell was leaving. "Can I have a word?" he asked, watching Elizabeth walk off to her office. Caldwell nodded and they walked back into the briefing room.

"Go ahead Sheppard," Caldwell said. John took a steadying breath, whilst being simultaneously irritated with himself that he had to do so.

"I'm," he paused. "I'm compromised, sir." Caldwell's eyes widened for a moment in surprise, but otherwise he kept his expression neutral.

"What exactly are you saying Colonel?" he asked.

"I'd like to, temporarily, hand over military control of this base over to you," John gritted out, doing a poor job of hiding the fact that this was killing him.

"I-" John watched as Caldwell restrained himself from gloating. "Very well, I'll extend the Daedalus' stay by a few days, if the situation hasn't changed by then I'll have Lorne take temporary command," he said.

"Yes sir," John agreed, only letting himself relax when Caldwell was out of sight, he dropped into the nearest chair and ran an agitated hand through his hair. After a few moments he stood up again and strode out of the room.

* * *

"You look like crap," Sheppard said as he entered the lab, Rodney didn't bother looking up from the computer screen.

"Hmmm," he agreed. "No worse than you're feeling, I doubt," he commented. Sheppard paused mid-step and Rodney looked up at him. "I- sorry. I shouldn't have said that," he apologised quietly, and looked back at the screen.

"N-o-o," Sheppard drawled, as he walked round the bench Rodney was sitting at and glanced at random items with an almost bored curiousness. Rodney studiously ignored him. "So," he said, waiting for Rodney to look up. He didn't. "When was the last time you got any sleep?"

"When was the last time you did?" Rodney countered. Sheppard frowned.

"I guess I'll have plenty of time for that now," Sheppard said, turning away from Rodney and glancing at a white board of equations. Rodney looked up in annoyance.

"And what exactly is that cryptic statement supposed to mean?" he asked with an irritated sigh..

"What?" Sheppard asked distractedly as he erased a portion of one of the equations on the whiteboard with his thumb and reached for a nearby pen.

"And now you're doing my work for me?" Rodney asked incredulously. "What exactly is the reason for your sudden limitless amounts of spare time?"

"Oh, I er," he paused as he scribbled a new set of numbers on the board. "I handed over command to Caldwell."

"Oh," he turned back to the laptop before looking up again at Sheppard. "Hang on!" He stood up, "You did what?"

"_Temporarily_, relinquished my command," he said as he capped the pen.

"This drove you crazy faster than I'd thought it would," Rodney muttered.

"Thanks Rodney, for those wonderful words of encouragement," Sheppard said sarcastically, snagging himself a stool and dropping down onto it.

"Seriously Sheppard, why?"

"I felt I was incapable of doing my job," Sheppard shrugged as he idly swung his legs back and forth.

"Don't be a ridiculous. A little off you game, maybe. But incapable?"

"Rodney," Sheppard said warningly. "Drop it." Rodney looked at him wide-eyed for a moment before nodding and sitting back down.

They sat in a companionable silence, which was only broken for a few moments with a stream of muttered Czech as Zelenka walked in, looked at the whiteboard, and walked out again. Rodney and Sheppard shared a grin before Rodney turned back to his work and Sheppard hopped off the stool and exited the labs.


	3. Chapter 3

When Elizabeth called him and McKay to her office, John knew he wasn't going to like whatever it was she had to say. Despite the fact that that was more often than not the case when he was called to her office, he just had a feeling that this time in particular was not going to be one of his favourites.

He wasn't disappointed.

"The planet's been cleared," she told them; John sat stiffly in his seat, Rodney was leaning forward more casually, arms on his thighs. Neither needed to ask which planet she was talking about. "There's a team gearing up as we speak."

She paused as they sat and looked at her expectantly. McKay rolled his hand in impatience and John smiled at the surprisingly reassuring, familiar gesture.

"Major Lorne is heading up a team of marines, along with Teyla and Ronon," she told them.

"I should be-" John began, but she cut him off.

"You resigned remember?" she said pointedly. From the tone of her voice he could tell she wasn't happy that he had forgone discussing it with her first, and that she had had to hear it from Caldwell, thus he resisted from saying that he'd actually taken a temporary leave of absence. He didn't think she'd appreciate the difference at the moment. Rodney shot him a sympathetic glance.

"It'd be boring anyway, they're probably just doing a sweep of the area around the gate and the facility, or where it used to be," he said with a lopsided smile in John's direction.

"Yes," Elizabeth nodded. "We're going to send a UAV to scan the rest of the planet," she added.

"Right, puddlejumper wouldn't get past all the trees," Rodney said with a wave of his hand. Elizabeth nodded.

"No, unfortunately not," she said. "I thought you should be apprised of the situation," she said with a smile.

"Thanks," John said, throwing her a smile he hoped looked sincere, but probably wasn't. "If that's all-?" he asked, standing up. Elizabeth shook her head, preventing John from making a hasty retreat. He felt both Rodney's concerned eyes on him as he left them to it.

"John," she said before sighing and shifting her eyes heavenward, as though asking for help with her words. "I understand why you stepped down," she said at last.

"Good, I-"

"But I disagree with your decision, at least at this point. Your style of command is preferable for Atlantis even if it was delivered in your sleep in comparison to Stephen's," she admitted with a smile. John ducked his head, uncomfortable with the praise, whilst simultaneously shoving down the desire to preen, alien in it's sudden intensity.

"This city would be a completely different place without you as its military commander. The way you treat and interact with the civilians here has set an example for everyone under your command; an example which most have chosen to follow," she continued.

"Elizabeth," he protested.

"What I'm trying to say, is that I don't want to lose that. We are not going to lose you, or Rodney.

John found the steely tone of conviction in her voice more comforting than he would have been willing to admit.

* * *

"Elizabeth!" Rodney called as he jogged to catch up with her as she left the commissary.

"Rodney," she greeted him with a nod as they continued walking.

"Did you get my email?"

"About the matter trans-"

"Matter transformer. It's not important, we can change the name later. Thing is, its an amazingly interesting piece of technology. I mean it can actually rearrange-"

"Rodney," she interrupted. "I don't doubt that it is amazing," she said sincerely, "But is it really what you should be concentrating right now?"

"I don't see why not," he shrugged.

"Perhaps your efforts would be best focused on the Ancient database?" she asked. "I hear Colonel Sheppard is helping out the team involved," she told him.

"He is?" Rodney asked, looking surprised for about a second before adding, "Well its not like he has anything else to do," and waving a hand dismissively. "So, back to the matter at hand?" he asked.

Elizabeth sighed and nodded as he began to explain the newly discovered piece of Ancient technology.

* * *

John was sitting at a work stations in one of the science labs. Zelenka had explained how they'd designed a search program to locate any relevant information that might exist in the database. The results were then translated into English and sent to the terminal John was working at. Thus far they hadn't found anything that would help them.

He had volunteered to help out because he was bored. But now he wished he hadn't, because he'd much rather be bored than depressed. They'd been running this search for eight days and weren't even point one of a percent through the database. At this rate it was going to take over twenty years to get through it all.

If he was honest with himself, John doubted they'd find anything. What Duyell had done had been against the rest of the Ancients wishes. It was possible they hadn't even known about it until he managed to ascend himself, in which case no details would have ever been recorded in the database.

But he didn't want to give up. Not outwardly anyway. Internally he'd already begun thinking about what he'd do when they shipped him back to earth. But he had to keep up appearances, for Rodney's sake, if not for his own.

* * *

"Hey Rodney!" Cadman called as she walked into his lab.

"Yes?" he responded without looking away from the data pad he was holding.

"I'm here to escort you to the infirmary," she told him.

"I don't need an escort," he said, glancing briefly at her. "I can walk."

"Then why haven't you gone? Carson said he's called you on the radio repeatedly, as has Colonel Sheppard," she said, walking further into the lab. Rodney waved his hand towards the bench, where his radio was sitting. "Why've you taken it off?" she asked frowning.

"Because they were getting on my nerves," he told her. She shook her head.

"Come on, lets just go down to the infirmary," she said.

"I'm fine, thanks," he said and sat down and began typing on one of the laptops.

"You're not fine McKay," she said sternly. "Pretending like you are isn't going to make it better." He finally looked up and glared at her in a way completely altered from the usual, something darker replaced the irritation that usually danced in his eyes.

"And what would you know about it?" he said, and stood up.

"Rodney-" she began placatingly as he stalked towards her.

"Just because Sheppard's given up on himself and let this beat him, doesn't mean I have to," he said angrily, having now backed her up against a desk.

"It's just a check-up Rodney!" she exclaimed as he grabbed her wrists in a vice-like grip.

"And," he continued as if she hadn't spoken, "I'm fed up with you people telling me what I should and shouldn't be doing!" he shouted, having now backed her up against a desk.

"Rodney, you need to calm-"

"No," he glared and pushed her hard enough against the bench to leave bruises on her back to match the ones likely to form on her wrists. His eyes widened for a moment and his grip loosened. "Just leave me the fuck alone," he muttered.

"Rodney!" an exclamation from the doorway had them both looking in that direction. "What's going on here?" Elizabeth demanded. Colonel Sheppard stood at her side frowning, his eyes darting to where Rodney's hands were wound round Cadman's wrists. He let go abruptly.

"I-" Rodney glanced to Cadman, who was rubbing at her sore wrists. "Sorry," he said to her, not able to look her in the eye.

There was a moment of tense silence before Sheppard walked into the lab.

"Come on Rodney," he said, patting him reassuringly on the back. "Let's go see Carson."

"I- Maybe that's a good idea, yeah," he said quietly, and let Sheppard steer him out of the room.


	4. Chapter 4

Two hours later they were all gathered in the briefing room.

"This is getting to be a problem," Elizabeth said.

"You're telling me," Rodney muttered as he fiddled with the Band-Aid on his arm where Carson had taking some blood earlier.

"I would have thought my temporary resignation would have already clued you into that fact," Sheppard said with a raised eyebrow.

"On that note," Elizabeth looked toward Colonel Caldwell.

"We can only justify staying for another few days," he said. "In which case Major Lorne will take temporary command, and we'll start looking for a suitable candidate to ship out from Earth, just in case," he added

"Sounds like a plan," Sheppard nodded, and got a few startled looks in response.

"This isn't helping us solve the problem," Rodney said.

"No," Elizabeth said slowly. "But you've yet to explain to us exactly what the problem is," she paused. "All we know is that it isn't a biological problem," she added glancing to Beckett who nodded.

"Aye, all tests back normal."

"So, gentlemen?" Elizabeth said expectantly.

"Its-" Sheppard began, glancing at Rodney. "Well you know how you know how you're going to react to certain things, how you're going to behave when someone irritates you or upsets you or…" he trailed off.

"We don't," Rodney said bluntly. "I have no idea how I'm going to react to anything from one minute to the next."

"Which is why I felt the need to step down as military commander. I'm going to be no good in the field if I suddenly have an emotional breakdown because I miss a shot," Sheppard said with a self-depreciating smile.

Elizabeth looked a little lost for words for a moment, shocked by their blunt honesty.

"If I may, it sounds to me like the early stages of emotional development in children," Kate Heightmeyer said. "Maybe its merely a process of getting used to these new emotional responses," she suggested.

Rodney glanced at Sheppard, they both knew it wasn't, couldn't be that simple. Apparently Elizabeth read their expressions.

"There's something else, isn't there?" she asked. Rodney watched as Sheppard ducked his head and avoided her eyes. It looked like it was up to Rodney to field this one.

"It hurts," he managed to choke out, he swallowed. "Like when you're upset and you get choked up, it, but ten times worse. And all the time," he told them. He heard Sheppard laugh quietly and looked at him.

"Rodney, we're going to die of broken hearts," he laughed bitterly.

"Die?" Rodney said quietly.

"You don't feel it?" Sheppard asked.

"Feel what?" Carson asked, concern entrenched in his tone.

"Like we're slipping further and further away," Rodney answered quietly.

They'd left the briefing with strict instructions to return to Carson for check-ups regularly, and to attend appointments with Heightmeyer. It was a show of how serious the situation was that neither of them had argued.

John was currently sitting in one of the labs, continuing to sift through the data the search of the database threw up. Zelenka was then sifting through the data John had deemed relevant. There was a lot of muttering that John didn't understand, but most of it sounded like cursing, so he doubted Radek was having that much luck.

They'd called Rodney on the radio several times, but had received no answer. John had thought the methodical nature of the task might have been relaxing for Rodney, and so had continued to try when Radek had given up. But it had proved futile and he'd eventually given up as well.

"John?" Elizabeth's voice came over the radio.

"Here," he responded.

"Lorne and the team have returned from the planet," she informed him. He didn't need to ask if they'd found anything, the tone of her voice said it all.

"Okay," he replied, eyes flickering over the screen in front of him.

"I was intending to call a briefing," she began.

"But?"

"But we can't get hold of Rodney on the radio," she said. "We checked the life signs detector, he's in his quarters," she told him. "I was wondering if you'd go and speak to him," she said hopefully.

"I don't know if I'm the right person for that Elizabeth," he said hesitantly.

"John," she said, and she was using That Tone. He hated that tone. "You know full well you're the best person to-"

"Yes, fine," he cut her off impatiently. "I'm on my way," he said, and closed the channel before she had a chance to respond.

When John opened the door to Rodney's quarters all the lights were out. He walked in, closing the door behind him and giving his eyes a chance to adjust. Only then did he spot Rodney sitting on the floor in the corner of the room, one leg bent with his arm resting on it and his head resting on his arm.

John walked over and sat down next to him. When Rodney looked up with red-rimmed eyes it wasn't surprising that he felt the compulsion to hug him, but the fact that he had to fight that compulsion ten times as hard as he might have otherwise was. He compromised by resting a hand on his shoulder.

Rodney squeezed his eyes shut and moved his face back to the confines of the crook of his arm.

"This is completely undignified and unmanly behaviour," he said unhappily into his arm, making John smile.

"Brains reprogrammed by a crazy alien," he reminded him.

"Still," Rodney muttered before they lapsed into a comfortable silence. After a few minutes Rodney sat up and looked at him. "We should get to that briefing?" he asked.

"Yeah," John nodded.

"Okay then," Rodney said, stood up and offered John a hand to pull him to his feet.

"We searched the area thoroughly, but there was nothing remaining," Teyla said.

"The UAV didn't pick up any energy readings," Elizabeth told them.

"Sorry, sir," Lorne said, looking towards Sheppard.

"Well it's not like we expected to find anything," Rodney said. "But something had to be done, for appearances at least."

"Rodney," Elizabeth chastised.

"Come on Elizabeth, we knew damn well they wouldn't find anything. But you couldn't just stand by and watch our gradual descent into insanity, so-"

"Rodney, shut up," Sheppard snapped in irritation. "You're not helping the situation."

"Not helping the-? At least I'm facing up to the situation. We are slowly drifting into a big dark void of nothingness. I'm sorry if I'm a little tetchy!" he exclaimed. He flinched as Sheppard grabbed his wrist in a vice like grip.

"Stop," he said roughly. Rodney took a deep breath.

"Right. Only panic about the things that might kill us, not the things that definitely will. I can do that," he said. "I used to do that," he added with an ironic smile.

"Good," Sheppard muttered, releasing Rodney's arm.

"Now," Rodney said, looking round the room of subdued onlookers. "We've decided to be positive," he said glancing at Sheppard who raised an eyebrow. "Or at least less negative," he amended. "So lets-"

Unfortunately, the rest of the Lanteans gathered in the room didn't get to hear what Rodney thought they should do, as both he and Sheppard disappeared in a flash of bright white light.  
.


End file.
